Pilot Projects for a Human Cell Atlas

We funded 38 pilot projects to help build new technologies, best practices, and data analysis techniques in support of the Human Cell Atlas. These individuals and organizations will accelerate our understanding in key areas including the brain, skin, and immune system; tissue handling and processing; and technological development.

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Showing 38 results

3D Volumetric, High Parameter, Iterative Imaging
Lead Investigator Garry Nolan
Institution Stanford University, United States
Focus Gastrointestinal
A Strategy for Mapping the Human Spinal Cord with Single-Cell Resolution
Lead Investigator Tom Maniatis
Institution Columbia University, United States
Focus Brain
Adversarial Training of Single-Cell RNA-seq: New Machine Learning Framework for Data Normalization & Visualization
Lead Investigator James Zou
Institution Stanford University, United States
Focus Technology Development
An Atlas of Airways at a Single-Cell Level
Lead Investigator Pascal Barbry
Institution CNRS - Université Côte D’Azur, France
Focus Tissue Handling and Processing
Assessing the Relevance of Organoids to Model Inter-Individual Variation
Lead Investigator Barbara Treutlein
Institution Max Planck Institute for Evolutionary Anthropology, Germany
Focus Brain
Cell and Tissue Preservation to Construct a Human Cell Atlas
Lead Investigator Seung Kim
Institution Stanford University, United States
Focus Gastrointestinal
Comparative Studies of Large-Scale Single-Cell Sequencing Technologies in Complex Tissues with Integrated On-Chip Imaging
Lead Investigator Peter Sims
Institution Columbia University, United States
Focus Immune
Comparing Microfluidic-Based Single-Cell RNA-seq Approaches for Development of a Human Kidney Cell Atlas
Lead Investigator Benjamin Humphreys
Institution Washington University in St. Louis, United States
Focus Tissue Handling and Processing
Comparison, Calibration, and Benchmarking of High-Throughput Single-Cell RNA-seq Techniques
Lead Investigator Anindita Basu
Institution University of Chicago, United States
Focus Tissue Handling and Processing
Developing Methodology to Assess Immune Cell Heterogeneity
Lead Investigator Menna Clatworthy
Institution University of Cambridge, United Kingdom
Focus Immune
Developing Psychrophilic Protease Methods for Tissue Dissociation
Lead Investigator Steven Potter
Institution Cincinnati Children’s Hospital, United States
Focus Tissue Handling and Processing
Developing Robust Methods to Process Solid Tissues for Single-Cell RNA-sequencing
Lead Investigator Jonathan Keats
Institution Translational Genomics Research Institute, United States
Focus Skin
Development of Site-Specific DNA-barcoded Antibodies for One-Pot Proteomics, Transcriptomics, and Interactomics
Lead Investigator James Wells
Institution University of California, San Francisco, United States
Focus Technology Development
Dyp-FISH: Dynamic Patterned FISH to Interrogate mRNA and Protein Subcellular Spatial Patterning
Lead Investigator Musa Mhlanga
Institution University of Cape Town, South Africa
Focus Technology Development
Enhanced Labeling and Barcode Expression of Virally Infected Cells
Lead Investigator Constance Cepko
Institution Harvard Medical School, United States
Focus Brain
Enhanced, Massively Parallel, and Multimodal Profiling for the Human Cell Atlas
Lead Investigator Rahul Satija
Institution New York Genome Center, United States
Focus Immune
Evaluation of Targeted-Nuclease Mapping of the Cell Type Specific Chromatin Landscape
Lead Investigator Steven Henikoff
Institution Fred Hutchinson Cancer Research Center, United States
Focus Immune
Human Fetal Tissue Preparation for scRNA-seq and Spatial Transcriptomics
Lead Investigator Sten Linnarsson
Institution Karolinska Institutet, Sweden
Focus Tissue Handling and Processing
In situ Interrogation of Epigenetic States in Single-Cells
Lead Investigator Joshua Vaughan
Institution University of Washington, United States
Focus Immune
Integrated Computational and Experimental Approaches to Dissect Cell Type Variation
Lead Investigator Evan Macosko
Institution Broad Institute of MIT and Harvard, United States
Focus Brain
Integration of Single-Cell Genomics and Spatial Proteomics
Lead Investigator Emma Lundberg
Institution KTH Royal Institute of Technology, Sweden
Focus Gastrointestinal
Microfluidic Platform for Rapid and Efficient Isolation of Single-Cells From Tissue
Lead Investigator Jered Haun
Institution University of California, Irvine, United States
Focus Tissue Handling and Processing
Modeling Post-Acquisition Tissue Stability for Single-Cell RNA-sequencing
Lead Investigator Kerstin Meyer
Institution Wellcome Sanger Institute, United Kingdom
Focus Tissue Handling and Processing
Multi-Scale Dissection of Rare Human Cellular Hierarchies
Lead Investigator Ido Amit
Institution Weizmann Institute of Science, Israel
Focus Immune
Multiplex Strategies for Fluorescence and Imaging Mass Cytometry for Image-Based Analyses
Lead Investigator Scott Fraser
Institution University of Southern California, United States
Focus Technology Development
Multiplexing Droplet-Based Single-Cell RNA-sequencing of Peripheral Blood Mononuclear Cells
Lead Investigator Jimmie Ye
Institution University of California, San Francisco, United States
Focus Immune
Non-Enzymatic Exponential Signal Amplification Probes for RNA in situ Hybridization
Lead Investigator Arjun Raj
Institution University of Pennsylvania, United States
Focus Technology Development
Optimized Isolation and Visualization of Human Skin Cells
Lead Investigator Fiona Watt
Institution King’s College London, United Kingdom
Focus Skin
Optimizing Early Post-Mortem Brain Cell Isolation for the HCA
Lead Investigator Michelle Monje
Institution Stanford University, United States
Focus Brain
Single-Cell Epigenetic State Profiling and Analysis with ATAC-seq In Complex Human Tissue
Lead Investigator William Greenleaf
Institution Stanford University, United States
Focus Gastrointestinal
Single-Cell RNA-seq Analysis of Human Brain Tissue
Lead Investigator Genevieve Konopka
Institution University of Texas, United States
Focus Brain
Single-Cell RNA-sequencing Tools to Evaluate and Enhance Experimental Replicability of the Human Cell Atlas
Lead Investigator Samantha Morris
Institution Washington University in St. Louis, United States
Focus Gastrointestinal
SpaceTx: Benchmarking Methods for Spatial Transcriptomic Mapping of Cortical Cell Types
Lead Investigator Ed Lein
Institution Allen Institute for Brain Science, United States
Focus Brain
SPAN: Spatial Pilot PANcreas
Lead Investigator Roland Eils
Institution Charité Universitätsmedizin, Germany
Focus Gastrointestinal
START: Standardization of Single-Cell and Single-Nucleus RNA-seq Protocols for Tumors
Lead Investigator Mario Suva
Institution Massachusetts General Hospital, United States
Focus Tissue Handling and Processing
Systematic Assessment of Single-Cell RNA-sequencing Protocols, Datasets and Analysis Methods
Lead Investigator Xuegong Zhang
Institution Tsinghua University, China
Focus Technology Development
The Human Breast Cell Atlas
Lead Investigator Nicholas Navin
Institution The University of Texas MD Anderson Cancer Center, United States
Focus Tissue Handling and Processing
Towards a Human Cardiac Cell Atlas
Lead Investigator Norbert Hübner
Institution Max-Delbruck Center for Molecular Medicine, Germany
Focus Tissue Handling and Processing

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